Download Dr. Amit Basak - Department of Chemistry, IIT Kgp

First Year Chemistry
Theory (Organic)
Starting date: 20 th October (Every Mon, Wed, Thu)
Finishing Date: 17th November
Teacher:
Prof. A. Basak
Reference book: Clayden/T.W.G. Solomons
Peter Sykes
Topics to be covered:
1) Structure / stereochemistry
2) Ionic rxns– addition/ elimination/substitution/
rearrangements
3) Free radical reactions
4) Concerted reactions(Diels Alder/electrocyclic)
5) Amino acids /peptides/enzymes (chymotrypsin)
6) Carbohydrates/ nucleic acids
Lecture 1
Why read organic chemistry?
O





Life is organic chemistry
Organic chemistry is the
chemistry of the compounds of
carbon
Deoxyribonucleic acids or DNA
RNA
Proteins
R1
O
H
N
H2N
N
H
O
R2
Base
O
O
O
O
Drug molecules:
P
O
O
O
Base
O
NHCOCH 3
H
N
R
OCOCH3
H
H
S
CH3
COOH
O
N
CH3
O
COOH
Penicillins
OH
Aspirin
Paracetamol
H 3C
COOH
Ibuprofen
Stereochemistry:
Chemistry in space, as a function of molecular geometry.
Constitution based chemistry:
OH
OH
OH
All these alcohols behave differently to certain reagents. That is due to
their different modes of connectivity.
A
B
A
C
X
X
C
D

B
D
x = functional group with same connectivity. However, reactivity of X
may differ again certain reagents.
OH
H
OH
Reactivity of the hydroxyl groups somewhat different.
H
Stereoisomerism
Isomerism
constitutional
chain
C-C-C-C
C-C-C
stereo
C-O-C
C-C-C
C - C -O
O
C - C- C
C
Enantiomers:
enantiomers diastereomers
positional
functional
O
Stereoisomers that are mirror images of one another
H3C
CH 3
COOH
HOOC
H
H
OH
OH
enantiomers
If a molecule is nonsuperimposable with its mirror image, then it
becomes optically active and is called a chiral molecule.
Chiral Centre (Asymmetric Centre): An atom, usually carbon
attached to four different ligands (atoms or groups)
Stereogenic Centre: An atom, again usually carbon, in
which interchanging the position of two ligands gives
rise to a stereoisomer.
This includes the carbon atom attached to four
different ligands as also the sp2 carbon which can
show cis-trans isomerism
X
Z
X
Me
C
C
Y
R
R
Y
Me
C
Z
Stereogenic centre
H
Me
C
H
C
H
H
Stereogenic centre
C
Me
Representation in 2D:
Projection Formula : Fischer, Newman………….
R
Fischer Projection :
R
Y
X
Y
X
Z
Suppose a molecule is drawn as :
Z
X
X
Z
R
Y
Y
X
R
R
Z
X
R
Rules:
Z
Y
Y
Z
(1) Exchange in a group of three allowed
X
R
X
Y
Z
Z
R
Y
(2) 1800 in plane rotation is allowed
Z
X
R
Y
Y
Z
(3) 900 in plane rotation
(4) 1800 out of plane rotation
R
X
?
Not Allowed
?
Not Allowed
Absolute configuration : The R,S - notation
(1)Assign priority sequence to the four groups attached to a
stereogenic carbon following the sequence rule.
(2) Observe the stereogenic centre from a direction opposite
to the group of lowest priority.
(3) Trace the path from 1 to 2 to 3
If clockwise
R ( rectus, right)
If anticlockwise
S (sinister, left)
1
1
S
4
3
2
R
4
3
2
Sequence Rules:
(1)If the four atoms directly attached to the stereogenic centre are different,
higher atomic number takes precedence over lower.
(3)
H3C
H
(4)
S
C
(1)Br
Cl (2)
(2) If the atoms directly attached to the stereocentre are same, then work
outward along the two chains atom by atom until a point of difference is
(1)
reached.
(4)
Br
CH 2CH 2CH3
s
CH3
Cl
(2)
CH 2CH
(3)
CH3
(3) Double and triple bonds are treated by assuming that each such
bonded atom is duplicated or triplicated.
O
O C
C H
C H
O
>
OH
C OH
H
CH CH2
C H
C C C >
H H
CH3
C H
CH3
What are absolute configurations of the following compounds :
O
H3CHC
HC
C
H3C
C
H
HC
H
OH
H
C
H3C
CN
H3C
Cl
More rules:
R
H
(2)
(4)
H
Br
Br
C
C
OH
R precedes S
Cl
(1)
(3)
S
S H
1
1
Br
CH3
2 Cl
H2
E precedes Z
cis precedes trans
1
2
Br
H
2 Cl
CH3
E
Z
Isotopic discrimination to
be applied only when
atomic no. fails
HO
CH2CD2CH3
C
H
CD2CH2CH3
C
CH2CH2CH3
1
CH2 CH
CH3
CH3